SAXSdb — 9vcm

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1. Protein Identity and Related Structures Protein Identity & Related Structures

NADH-dependent dihydrogenase

Amycolatopsis mediterranei S699

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	RifT × 2 （O52542） ;(4Z,6E,8S,9S,10R,11R,12R,13R,14R,15S,16S,17Z,22R,23S)-4,8,10,12,14,16,18,22-octamethyl-9,11,13,15,23,26,28-heptakis(oxidanyl)-2-azabicyclo[22.3.1]octacosa-1(27),4,6,17,24(28),25-hexaene-3,19,21-trione ; × 2 ADENOSINE MONOPHOSPHATE × 1 SULFATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O52541_AMYMD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–342； UniProt 1–342 Author chain C； PDBConstruct 1–342； UniProt 1–342

RifT

Amycolatopsis mediterranei S699

UniProt O52542

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	NADH-dependent dihydrogenase × 2 （O52541） ;(4Z,6E,8S,9S,10R,11R,12R,13R,14R,15S,16S,17Z,22R,23S)-4,8,10,12,14,16,18,22-octamethyl-9,11,13,15,23,26,28-heptakis(oxidanyl)-2-azabicyclo[22.3.1]octacosa-1(27),4,6,17,24(28),25-hexaene-3,19,21-trione ; × 2 ADENOSINE MONOPHOSPHATE × 1 SULFATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O52542_AMYMD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–256； UniProt 2–255 Author chain D； PDBConstruct 3–256； UniProt 2–255

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9vcm
Deposition date deposition_date	2025-06-06
Last revision last_revision	2026-06-10
Structure title title	NAD_dependent dehydrogenase
Keywords keywords	COMPLEX. NAD-DEPENDENT, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9vcm__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9vcm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9vcm__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	34.13 Å
Rg (electron density)	33.31 Å
Total Rg	33.97 Å
Atom count	8483
Residues	1151
Excluded volume	148920 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9vcm__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	NADH-dependent dihydrogenase
Molecular weight formula_weight	35368.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	8999

MAPTGGVGESRYVKTLRQLEVALIGAGLIARLHLEAWLGAGAAVRVYSDDGRSRELAAEFGAKAAGSLEEALDGADAVDICTPTASHHEIALTAIAAGVGVVCEKPLAASAEEAEEIVTAAERAGVRLYAAHDVRFAAPYARLHELVASGRLGEGALGRFSFSAYHPRPWTGHASARSGGILTDQLLHGADLAHWVFGDVVRVHACYQGDIATPAPEGAVATGTAVLTHASGAISQVVSRWTATPRPPVRVAFHVSGTGGSVSYDSEWPQEVRVVDGGAGNFAYGGPSVFDTEMREFATAFAGGPEPRIGAKDALAAVRIIHAAAESAWTGRAVELPVRGAA

Source Source

Source organism organism	Amycolatopsis mediterranei S699
NCBI taxonomy ID ncbi_taxonomy_id	713604
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	RifT
Molecular weight formula_weight	26214.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MVKVAILSSTPQAYAGALRGLPDVEVVAAASWDAFEPVRQAAEAGARVLCEYPPAAKETDLKAMIDAAGDRLTFASPACHGEAFAVVRKGIADGGIGELTTVLGSVATSVDGVLGAAAPYLLDLADAVLGGEPAQQVYAQTNIVLSGRIGESAAVLTVRYRSGQVASFDCRRHGSATGLPAVTFIGDQGSVQYDAGPQLLGGERPELGGEDLEALMLKDFLGAGDGPGPDGQAALRTFRIIQAAYESAHTGQPVDL

Source Source

Source organism organism	Amycolatopsis mediterranei S699
NCBI taxonomy ID ncbi_taxonomy_id	713604
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	;(4Z,6E,8S,9S,10R,11R,12R,13R,14R,15S,16S,17Z,22R,23S)-4,8,10,12,14,16,18,22-octamethyl-9,11,13,15,23,26,28-heptakis(oxidanyl)-2-azabicyclo[22.3.1]octacosa-1(27),4,6,17,24(28),25-hexaene-3,19,21-trione ;
Molecular weight formula_weight	645.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	516

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Unit-cell length a length_a	192.182 Å
Unit-cell length b length_b	81.259 Å
Unit-cell length c length_c	90.126 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.84 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	28.990 Å
R factor r_factor	0.1780
R_work r_work	0.1760
R_free r_free	0.2280

NAD_dependent dehydrogenase

1. Protein Identity and Related Structures Protein Identity & Related Structures

NADH-dependent dihydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

RifT

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9vcm__assembly_1__model_1

9vcm__assembly_1__model_1 | I(q)

9vcm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

NAD_dependent dehydrogenase

1. Protein Identity and Related Structures Protein Identity & Related Structures

NADH-dependent dihydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RifT

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9vcm__assembly_1__model_1

9vcm__assembly_1__model_1 | I(q)

9vcm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)